{ "_id": "6ae761c2818c9e3ef6dbc05f", "Package": "GeneGA", "Type": "Package", "Title": "Design gene based on both mRNA secondary structure and codon\nusage bias using Genetic algorithm", "Version": "1.63.1", "Date": "2013-3-6", "Author": "Zhenpeng Li and Haixiu Huang", "Maintainer": "Zhenpeng Li ", "biocViews": "GeneExpression", "Description": "R based Genetic algorithm for gene expression optimization\nby considering both mRNA secondary structure and codon usage\nbias, GeneGA includes the information of highly expressed genes\nof almost 200 genomes. Meanwhile, Vienna RNA Package is needed\nto ensure GeneGA to function properly.", "License": "GPL version 2", "URL": "http://www.tbi.univie.ac.at/~ivo/RNA/", "Config/Bioconductor/UnsupportedPlatforms": "windows", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-05-29 18:37:29 UTC", "RemoteUrl": "https://github.com/bioc/GeneGA", "RemoteRef": "HEAD", "RemoteSha": "9e9d8f2feb23d2f00b263c04b7322919ab4f7968", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-01 13:37:53 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "GeneGA_1.63.1.tar.gz", "_fileid": "https://r2.ropensci.org/bf91ddc013e91c3aacb9a5e070ba02c08c91be5268be19e8c1278f8fcb0f281e", "_filesize": 195485, "_sha256": "bf91ddc013e91c3aacb9a5e070ba02c08c91be5268be19e8c1278f8fcb0f281e", "_expires": "2027-02-09T15:58:56.000Z", "_created": "2026-11-01T13:37:53.000Z", "_published": "2026-11-01T15:58:58.396Z", "_upstream": "https://github.com/bioc/GeneGA", "_status": "failure", "_maintainer": { "name": "Zhenpeng Li", "email": "zpli21@gmail.com" }, "_jobs": [ { "job": 124864801772, "time": 137, "config": "bioc-checks", "r": "4.6.2", "check": "ERROR", "artifact": "13087135598" }, { "job": 124864801796, "time": 232, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "13087160724" }, { "job": 124864801768, "time": 221, "config": "linux-release-x86_64", "r": "4.6.2", "check": "ERROR", "artifact": "13085659717" }, { "job": 124864801892, "time": 117, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "13090790920" }, { "job": 124864801776, "time": 112, "config": "macos-release-arm64", "r": "4.6.2", "check": "ERROR", "artifact": "13090541284" }, { "job": 124859542644, "time": 182, "config": "source", "r": "4.6.2", "check": "ERROR", "artifact": "13085546706" }, { "job": 124864801760, "time": 79, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13086741507" }, { "job": 124864801843, "time": 68, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "13086565541" }, { "job": 124864801806, "time": 60, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "13086217048" }, { "job": 124864802043, "time": 51, "config": "windows-release-x86_64", "r": "4.6.2", "check": "ERROR", "artifact": "13085726925" } ], "_bioccheck": { "error": 1, "warning": 4, "note": 17 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41309878035", "_commit": { "id": "9e9d8f2feb23d2f00b263c04b7322919ab4f7968", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "Bump version\n", "time": 1780079849 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "seqinr", "role": "Depends" }, { "package": "hash", "role": "Depends" }, { "package": "methods", "role": "Depends" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 }, { "week": "2026-22", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.63.1", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.62.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "geneexpression" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 482, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 400, "source": "https://www.bioconductor.org/packages/stats/bioc/GeneGA" }, "_searchresults": 10, "_abi": { "exports": [ { "key": "GeneGA::GeneFoldGA", "hash": "3761f3066836f4ae" }, { "key": "GeneGA::GeneGA", "hash": "7d4946c8b538ea00" }, { "key": "GeneGA::generic:plotGeneGA", "hash": "54e285551c804f1a" } ], "imports": [] }, "_rbuild": "4.6.2", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GeneGA.html", "extra/manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "GeneCodon", "GeneFoldGA", "GeneGA", "plotGeneGA", "show" ], "_datasets": [ { "name": "wSet", "title": "Codon Adaptation Index (CAI) w tables", "object": "wSet", "file": "wSet.rda", "class": [ "data.frame" ], "fields": [ "aaa", "aac", "aag", "aat", "aca", "acc", "acg", "act", "aga", "agc", "agg", "agt", "ata", "atc", "atg", "att", "caa", "cac", "cag", "cat", "cca", "ccc", "ccg", "cct", "cga", "cgc", "cgg", "cgt", "cta", "ctc", "ctg", "ctt", "gaa", "gac", "gag", "gat", "gca", "gcc", "gcg", "gct", "gga", "ggc", "ggg", "ggt", "gta", "gtc", "gtg", "gtt", "taa", "tac", "tag", "tat", "tca", "tcc", "tcg", "tct", "tga", "tgc", "tgg", "tgt", "tta", "ttc", "ttg", "ttt" ], "rows": 200, "table": true, "tojson": true } ], "_help": [ { "page": "GeneGA-package", "title": "Designing gene based on mRNA secondary structure and codon usage bias using Genetic algorithm, GeneGA includes the information of highly expressed genes of almost 200 genomes.", "topics": [ "GeneGA-package" ] }, { "page": "GeneCodon", "title": "Optimizing the codon usage of gene by replacing less usage codons with the most preference used codons or replacing the most preference used codons with less usage codons.", "topics": [ "GeneCodon" ] }, { "page": "GeneFoldGA", "title": "the function optimizes gene merely considering mRNA secondary structure.", "topics": [ "GeneFoldGA" ] }, { "page": "GeneFoldGA-class", "title": "Class \"GeneFoldGA\"", "topics": [ "GeneFoldGA-class", "show,GeneFoldGA-method" ] }, { "page": "GeneGA", "title": "the function optimizes gene expression based on both mRNA secondary structure and codon usage bias", "topics": [ "GeneGA" ] }, { "page": "GeneGA-class", "title": "Class \"GeneGA\"", "topics": [ "GeneGA-class", "show,GeneGA-method" ] }, { "page": "plotGeneGA-methods", "title": "plotGeneGA methods of GeneGA and GeneFoldGA objects", "topics": [ "plotGeneGA", "plotGeneGA,GeneFoldGA-method", "plotGeneGA,GeneGA-method", "plotGeneGA-methods", "plotGeneGA.GeneFoldGA", "plotGeneGA.GeneGA" ] }, { "page": "wSet", "title": "Codon Adaptation Index (CAI) w tables", "topics": [ "wSet" ] } ], "_rundeps": [ "ade4", "hash", "lattice", "MASS", "nlme", "pixmap", "Rcpp", "RcppArmadillo", "segmented", "seqinr", "sp" ], "_score": 2.4771212547196626, "_indexed": true, "_nocasepkg": "genega", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.63.1", "date": "2026-11-01T14:10:56.000Z", "distro": "resolute", "commit": "9e9d8f2feb23d2f00b263c04b7322919ab4f7968", "fileid": "https://r2.ropensci.org/9286093da2c95da98d2daa9461c28a01acecf71b0690a466700f11184b181b71", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309878035" }, { "r": "4.6.2", "os": "linux", "version": "1.63.1", "date": "2026-11-01T14:10:49.000Z", "distro": "resolute", "commit": "9e9d8f2feb23d2f00b263c04b7322919ab4f7968", "fileid": "https://r2.ropensci.org/bd713fcace4da7082fb378389b1178e9e5ffbc7bfc35840327ec6dc218884862", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309878035" }, { "r": "4.5.3", "os": "mac", "version": "1.63.1", "date": "2026-11-01T15:58:25.000Z", "commit": "9e9d8f2feb23d2f00b263c04b7322919ab4f7968", "fileid": "https://r2.ropensci.org/1642bf81303587b0450f2a7c95c845930a650a2baaa0f30940b23a787638251e", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309878035" }, { "r": "4.6.2", "os": "mac", "version": "1.63.1", "date": "2026-11-01T15:58:17.000Z", "commit": "9e9d8f2feb23d2f00b263c04b7322919ab4f7968", "fileid": "https://r2.ropensci.org/8ec263d790423b437244075c95798e4621982f064d8b06935696f3a217ebebf3", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309878035" }, { "r": "4.6.0", "os": "wasm", "version": "1.63.1", "date": "2026-11-01T14:08:40.000Z", "commit": "9e9d8f2feb23d2f00b263c04b7322919ab4f7968", "fileid": "https://r2.ropensci.org/b900046d7d71febc395f00ddc608e7a1915cd43fd7658b557f6122fcce29495a", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309878035" }, { "r": "4.7.0", "os": "win", "version": "1.63.1", "date": "2026-11-01T13:44:02.000Z", "commit": "9e9d8f2feb23d2f00b263c04b7322919ab4f7968", "fileid": "https://r2.ropensci.org/00d04771316a94d4a3133a4591009705f84c1a810b10c7bb2136aec47950fdb7", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309878035" }, { "r": "4.5.3", "os": "win", "version": "1.63.1", "date": "2026-11-01T13:43:57.000Z", "commit": "9e9d8f2feb23d2f00b263c04b7322919ab4f7968", "fileid": "https://r2.ropensci.org/49cc00017f7a258e229b818c0e3c2a923709816b35d9b98d3493b4a60fe0a472", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309878035" }, { "r": "4.6.2", "os": "win", "version": "1.63.1", "date": "2026-11-01T13:43:52.000Z", "commit": "9e9d8f2feb23d2f00b263c04b7322919ab4f7968", "fileid": "https://r2.ropensci.org/32c56f49a0558639f9b1d48e027ce2b6846cde0a8073fc394d8539e979016ad4", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309878035" } ] }